WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis

Ghislain Bidaut, Frank J. Manion, Christophe Garcia, Michael F. Ochs

Research output: Contribution to journalArticle

Abstract

Gene expression microarrays monitor the expression levels of thousands of genes in an experiment simultaneously. To utilize the information generated, each of the thousands of spots on a microarray image must be properly quantified, including background correction. Most present methods require manual alignment of grids to the image data, and still often require additional minor adjustments on a spot by spot basis to correct for spotting irregularities. Such intervention is time consuming and also introduces inconsistency in the handling of data. A fully automatic, tested system would increase throughput and reliability in this field. In this paper, we describe WaveRead, a fully automated, standalone, open-source system for quantifying gene expression array images. Through the use of wavelet analysis to identify the spot locations and diameters, the system is able to automatically grid the image and quantify signal intensities and background corrections without any user intervention. The ability of WaveRead to perform proper quantification is demonstrated by analysis of both simulated images containing spots with donut shapes, elliptical shapes, and Gaussian intensity distributions, as well as of standard images from the National Cancer Institute.

Original languageEnglish (US)
Pages (from-to)379-388
Number of pages10
JournalJournal of Biomedical Informatics
Volume39
Issue number4
DOIs
StatePublished - Aug 2006
Externally publishedYes

Fingerprint

Wavelet Analysis
Wavelet analysis
Microarrays
Gene expression
Gene Expression
Metrorrhagia
National Cancer Institute (U.S.)
Normal Distribution
Genes
Throughput
Experiments

Keywords

  • Image analysis
  • Microarrays
  • Wavelet decomposition

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics
  • Computer Science (miscellaneous)
  • Catalysis

Cite this

WaveRead : Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. / Bidaut, Ghislain; Manion, Frank J.; Garcia, Christophe; Ochs, Michael F.

In: Journal of Biomedical Informatics, Vol. 39, No. 4, 08.2006, p. 379-388.

Research output: Contribution to journalArticle

Bidaut, Ghislain ; Manion, Frank J. ; Garcia, Christophe ; Ochs, Michael F. / WaveRead : Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. In: Journal of Biomedical Informatics. 2006 ; Vol. 39, No. 4. pp. 379-388.
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